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Crystal structure of rifampin phosphotransferase rph-lm from listeria monocytogenes in complex with rifampin-phosphate

Analyse Crystal structure of rifampin phosphotransferase rph-lm from listeria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FBU
Type: protein
Length: 733 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoenolpyruvate synthase
Ligands: 5WP, CL
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoenolpyruvate synthase	protein	733	48% helix, 11% strand	—

Ligands and binding sites

5WP · Rifampin-phosphate · ligand · chains A
CL · Chloride ion · ion · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	935	0.78	0.80	111	empty
2	946	0.74	0.77	69	5WP
3	290	0.58	0.77	40	empty
4	181	0.46	0.75	32	empty
5	103	0.44	0.78	25	empty

Compared structures

5FBU · Crystal structure of rifampin phosphotransferase RPH-Lm from Listeria monocytogenes in… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5FBU · PDBe 5FBU

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